Applicability of Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers in assessing genetic diversity in Crepidium acuminatum (D. Don) Szlach.

Thakur, Julie; Dwivedi, Mayank D.; Singh, Navneet; Uniyal, Prem L.; Goel, Shailendra; Pandey, Arun K.

doi:10.1016/j.jarmap.2021.100310

Cited by 10 publications

(4 citation statements)

References 33 publications

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“…Thus, the extensive use of neutral molecular markers targeting different regions is conducive to the comprehensive elucidation of plant genetic diversity and relationships ( Gogoi et al, 2020 ). To date, many applications combining multiple molecular marker techniques have been employed to evaluate the genetic diversity and genetic relationships of plants ( Antony et al, 2015 ; Thakur et al, 2021b ; Tikendra et al, 2021 ). The combination of 45 ISSR and SCoT primers produced a higher number of alleles (508) with an average of 69% and 78% (P), demonstrating the usefulness of the selected primers for identifying the genetic variability between the studied cultivars.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

ALshamrani

Safhi²,

Alshaya³

et al. 2022

Front. Genet.

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The genetic diversity and the relationships among sesame cultivars were investigated using physiological and cyto/molecular analysis. To our information, no studies have yet been conducted on the genetic evaluation of sesame genotypes based on cyto/molecular analysis in Saudi Arabia. This study showed that genotype Bah-312 had the highest values from physiological and biochemical traits (plant height, harvest index, total plant dry matter, seed yield, oil content, and fatty acids content). Using 20 ISSR and 25 SCoT primers, the studied genotypes amplified 233 and 275 alleles, while the average polymorphism percentage (P%) was 65.32% (ISSR) and 77.8% (SCoT) across all the studied genotypes, respectively. To assess the markers efficiency analysis the polymorphism information contents (PIC), Marker Index (MI), Effective Multiplex Ratio (EMR), Resolving Power (Rp) were estimated. In general, primers (ISSR 2 & SCoT 21) and (ISSR 4 & SCoT 3) revealed the highest and lowest values for P %, PIC, MI, and EMR%. Furthermore, 188 positive and negative unique bands were detected, out of which ISSR generated 84, while 104 were amplified by SCoT analysis. In this regard, genotype Bah-312 generated 41 unique amplicons, and Jiz-511 genotype 23 unique amplicons. In the same context, the population genetics parameters, number of different alleles (Na), number of effective alleles (Ne), Shannon’s index (I), expected heterozygosity (He), and Unbiased Expected Heterozygosity (uHe), were calculated. ISSR marker showed the highest values for all the estimated parameters. In this regard, genotype Bah-312 exhibited the highest values (1.35, 1.37, 0.31, 0.21, 0.29) & (1.31, 1.35, 0.30, 0.20, 0.27) while, genotype Ahs-670 revealed the least values (1.29, 1.31, 0.26, 0.16, 0.23) &(1.14, 1.26, 0.22, 0.15, 0.20) for ISSR and SCoT markers respectively. For cytological data, according to the highest asymmetry index (AsK%) and lowest total form percentage (TF%) values, genotype Ahs-670 was the most advanced cultivar, and genotype Bah-312 was the most primitive one. According to the degree of asymmetry of karyotype (A) and intrachromosomal asymmetry index (A1), sesame genotype Ahs-670 was the most asymmetrical, and Bah-312 was the most symmetrical genotype. This study gives some helpful information about the genetic diversity of six sesame landraces. The variation harbored by these landraces could be used in sesame breeding programs.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

ALshamrani

Safhi²,

Alshaya³

et al. 2022

Front. Genet.

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“…The population structure analysis showed that SCoT markers could not differentiate the two species of Tinospora from T. cordifolia accessions from Delhi, UP states. Similar studies with SCoT markers showed pure and admixture individuals in medicinal plants like Dendrobium and Crepidium with three (K = 3) and two (K = 2) populations, respectively [ 56 , 57 ]. AMOVA analysis showed a 4% variation among the population which was observed at 34% in Clerodendrum serratum [ 58 ].…”

Section: Discussionmentioning

confidence: 64%

Molecular Characterization of Tinospora cordifolia (Willd.) Miers Using Novel g-SSR Markers and Their Comparison with EST-SSR and SCoT Markers for Genetic Diversity Study

Paliwal

Singh

Choudhury

et al. 2022

Genes

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In the present study, novel genomic-SSR (g-SSR) markers generated in our laboratory were used to characterize Tinospora cordifolia and related species. The g-SSR marker was also compared with EST-SSR and SCoT markers used earlier in our laboratory to assess the genetic diversity of T. cordifolia. A total of 26 accessions of T. cordifolia and 1 accession each of Tinospora rumphii and Tinospora sinensis were characterized using 65 novel g-SSR markers. A total of 125 alleles were detected with 49 polymorphic g-SSR markers. The number of alleles per locus varied from 1–4 with a mean value of 2.55 alleles per locus. Mean PIC, gene diversity, and heterozygosity were estimated to be 0.33, 0.41, and 0.65, respectively. The two species, namely T. rumphii and T. sinensis, showed cross-species transferability of g-SSRs developed in T. cordifolia. The success rate of cross-species transferability in T. rumphii was 95.3% and 93.8% in T. sinensis, proving the usefulness of this marker in genetic diversity studies of related species. The Tinospora accessions were also used for molecular characterization using SCoT and EST-SSR markers and compared for genetic diversity and cross-species transferability. The PIC, gene diversity, heterozygosity, and principal coordinate analysis showed that g-SSR is the better maker for a genetic diversity study of T. cordifolia. Additionally, high cross-species transferability of g-SSRs was found (95.3% and 93.8%) compared to EST-SSRs (68.8% and 67.7%) in T. rumphii and T. sinensis, respectively.

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“…SCoT markers were usually reproducible but exceptions indicated that primer length and annealing temperature are not the sole factors determining reproducibility. SCoT marker PCR amplification profiles indicated dominant markers like RAPD markers (Collard and Mackill 2009a;Thakur et al, 2021).…”

Section: Start Codon Targeted (Scot) Markermentioning

confidence: 99%

Response of Different Tomato Accessions to Biotic and Abiotic Stresses

Rasul

2023

SSRN Journal

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Applicability of Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers in assessing genetic diversity in Crepidium acuminatum (D. Don) Szlach.

Cited by 10 publications

References 33 publications

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

Molecular Characterization of Tinospora cordifolia (Willd.) Miers Using Novel g-SSR Markers and Their Comparison with EST-SSR and SCoT Markers for Genetic Diversity Study

Response of Different Tomato Accessions to Biotic and Abiotic Stresses

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